htsjdk.samtools

Class BAMFileReader.BAMQueryFilteringIterator

java.lang.Object

htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator

All Implemented Interfaces:

CloseableIterator<SAMRecord>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<SAMRecord>

Enclosing class:

BAMFileReader

public class BAMFileReader.BAMQueryFilteringIterator
extends java.lang.Object

Pull SAMRecords from a coordinate-sorted iterator, and filter out any that do not match the filter.

Field Summary

Fields

Modifier and Type	Field and Description
protected SAMRecord	mNextRecord The next record to be returned.
protected CloseableIterator<SAMRecord>	wrappedIterator The wrapped iterator.

Constructor Summary

Constructors

Constructor and Description
BAMQueryFilteringIterator(CloseableIterator<SAMRecord> iterator, htsjdk.samtools.BAMIteratorFilter iteratorFilter)

Method Summary

Modifier and Type	Method and Description
boolean	hasNext() Returns true if a next element exists; false otherwise.
SAMRecord	next() Gets the next record from the given iterator.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

wrappedIterator

protected final CloseableIterator<SAMRecord> wrappedIterator

The wrapped iterator.

mNextRecord

protected SAMRecord mNextRecord

The next record to be returned. Will be null if no such record exists.

Constructor Detail

BAMQueryFilteringIterator

public BAMQueryFilteringIterator(CloseableIterator<SAMRecord> iterator,
                                 htsjdk.samtools.BAMIteratorFilter iteratorFilter)

Method Detail

hasNext

public boolean hasNext()

Returns true if a next element exists; false otherwise.

next

public SAMRecord next()

Gets the next record from the given iterator.

Returns:

The next SAM record in the iterator.